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#molecular_dynamics

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The BTS of the videos are here!

Cited articles

The main paper for this video

Boonserm, P., Somsoros, W., Khunrae, P., Charupanit, K., Limsakul, P., & Sutthibutpong, T. (2024). Allosteric Signal within the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein Mediated by a Class 3 Monoclonal Antibody Revealed through Molecular Dynamics Simulations and Protein Residue Networks. ACS omega, 9(4), 4684-4694.

More on the communicability matrix:

Arrigo, F.; Durastante, F. Mittag–Leffler Functions and their Applications in Network Science. SIAM J. Matrix Anal. Appl. 2021, 42 (4), 1581−1601, DOI: 10.1137/21M1407276.

In depth deep dive into molecular dynamics:

https://manual.gromacs.org/current/in...

a great PCA explanation video:
   • StatQuest: Principal Component Analys...  

@MoBioChem is also a great channel for explaining MD

Molecular Nodes is a 3D animation library created by @BradyJohnston

Here’s a link to the repo: https://github.com/BradyAJohnston/Mol...

big thanks!